Random network behaviour of protein structures

K. V. Brinda, Saraswathi Vishveshwara, Smitha Vishveshwara

Research output: Contribution to journalArticle

Abstract

Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus imperative that, apart from the protein backbone, other tunable degrees of freedom be accountable. Here, we focus on side-chain interactions, which non-covalently link amino acids in folded proteins to form a network structure. At a coarse-grained level, we show that the network conforms remarkably well to realizations of random graphs and displays associated percolation behavior. Thus, within the rigid framework of the protein backbone that restricts the structure space, the side-chain interactions exhibit an element of randomness, which account for the functional flexibility and diversity shown by proteins. However, at a finer level, the network exhibits deviations from these random graphs which, as we demonstrate for a few specific examples, reflect the intrinsic uniqueness in the structure and stability, and perhaps specificity in the functioning of biological proteins.

Original languageEnglish (US)
Pages (from-to)391-398
Number of pages8
JournalMolecular BioSystems
Volume6
Issue number2
DOIs
StatePublished - Feb 8 2010

Fingerprint

Proteins
Amino Acids

ASJC Scopus subject areas

  • Biotechnology
  • Molecular Biology

Cite this

Random network behaviour of protein structures. / Brinda, K. V.; Vishveshwara, Saraswathi; Vishveshwara, Smitha.

In: Molecular BioSystems, Vol. 6, No. 2, 08.02.2010, p. 391-398.

Research output: Contribution to journalArticle

Brinda, K. V. ; Vishveshwara, Saraswathi ; Vishveshwara, Smitha. / Random network behaviour of protein structures. In: Molecular BioSystems. 2010 ; Vol. 6, No. 2. pp. 391-398.
@article{a0b39b7085b64780a17713f5ff2ac83c,
title = "Random network behaviour of protein structures",
abstract = "Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus imperative that, apart from the protein backbone, other tunable degrees of freedom be accountable. Here, we focus on side-chain interactions, which non-covalently link amino acids in folded proteins to form a network structure. At a coarse-grained level, we show that the network conforms remarkably well to realizations of random graphs and displays associated percolation behavior. Thus, within the rigid framework of the protein backbone that restricts the structure space, the side-chain interactions exhibit an element of randomness, which account for the functional flexibility and diversity shown by proteins. However, at a finer level, the network exhibits deviations from these random graphs which, as we demonstrate for a few specific examples, reflect the intrinsic uniqueness in the structure and stability, and perhaps specificity in the functioning of biological proteins.",
author = "Brinda, {K. V.} and Saraswathi Vishveshwara and Smitha Vishveshwara",
year = "2010",
month = "2",
day = "8",
doi = "10.1039/b903019k",
language = "English (US)",
volume = "6",
pages = "391--398",
journal = "Molecular BioSystems",
issn = "1742-206X",
publisher = "Royal Society of Chemistry",
number = "2",

}

TY - JOUR

T1 - Random network behaviour of protein structures

AU - Brinda, K. V.

AU - Vishveshwara, Saraswathi

AU - Vishveshwara, Smitha

PY - 2010/2/8

Y1 - 2010/2/8

N2 - Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus imperative that, apart from the protein backbone, other tunable degrees of freedom be accountable. Here, we focus on side-chain interactions, which non-covalently link amino acids in folded proteins to form a network structure. At a coarse-grained level, we show that the network conforms remarkably well to realizations of random graphs and displays associated percolation behavior. Thus, within the rigid framework of the protein backbone that restricts the structure space, the side-chain interactions exhibit an element of randomness, which account for the functional flexibility and diversity shown by proteins. However, at a finer level, the network exhibits deviations from these random graphs which, as we demonstrate for a few specific examples, reflect the intrinsic uniqueness in the structure and stability, and perhaps specificity in the functioning of biological proteins.

AB - Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus imperative that, apart from the protein backbone, other tunable degrees of freedom be accountable. Here, we focus on side-chain interactions, which non-covalently link amino acids in folded proteins to form a network structure. At a coarse-grained level, we show that the network conforms remarkably well to realizations of random graphs and displays associated percolation behavior. Thus, within the rigid framework of the protein backbone that restricts the structure space, the side-chain interactions exhibit an element of randomness, which account for the functional flexibility and diversity shown by proteins. However, at a finer level, the network exhibits deviations from these random graphs which, as we demonstrate for a few specific examples, reflect the intrinsic uniqueness in the structure and stability, and perhaps specificity in the functioning of biological proteins.

UR - http://www.scopus.com/inward/record.url?scp=75749155822&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=75749155822&partnerID=8YFLogxK

U2 - 10.1039/b903019k

DO - 10.1039/b903019k

M3 - Article

C2 - 20094659

AN - SCOPUS:75749155822

VL - 6

SP - 391

EP - 398

JO - Molecular BioSystems

JF - Molecular BioSystems

SN - 1742-206X

IS - 2

ER -